Background <p>Gastric cancer (GC) is a highly aggressive and heterogeneous cancer with extremely complex biological characteristics. Lysine and its metabolism are closely related to human cancer, but little is known about how lysine metabolism-related genes contribute to gastric carcinogenesis.</p> Methods <p>The roles of lysine metabolism-related genes in GC were investigated by in-depth analysis of single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) data via machine learning and multiple bioinformatics methods and confirmed by multiple cell and molecular biology methods.</p> Results <p>By systematically analyzing the heterogeneity of GC cells and interactions among cell subtypes, two key genes, solute carrier family 7 member 7 (<i>SLC7A7</i>) and vimentin (<i>VIM</i>), were innovatively identified as lysine metabolism-related genes involved in gastric carcinogenesis. The potential functional mechanisms involved immune infiltration, signaling pathway regulation, drug sensitivity, molecular regulatory networks, tumor regulatory genes, and metabolic pathways. A reliable prognostic risk nomogram was established for GC prognosis prediction. Moreover, the expression of the lysine metabolism-related genes <i>SLC7A7</i> and <i>VIM</i> and their effect on cellular phenotypes in gastric carcinogenesis were verified in clinical samples and in vitro experiments, including cell proliferation, migration, invasion and cell cycle assays.</p> Conclusions <p>We explored the role of lysine metabolism-related genes and prognostic models in GC with multiple datasets, providing novel metabolic targets.</p>